Over the last 40 years, dissolved organic carbon (DOC) has been increasing in freshwater across many boreal regions. The extent to which these long-term changes have affected lake CO2 dynamics is unclear. We have studied the temporal trends in DOC and pressure of CO2 (pCO2) over 40 years in 15 lakes in two regions of Ontario (Canada) subjected to browning and the abatement of SO2 deposition. Whereas from 1980 to 1999 there were no significant trends in pCO2 in any of the lakes, a significant increase was observed from 2000 to 2017. Although DOC concentrations increased during the same period, pCO2 and DOC were only weakly coupled, and we hypothesize the existence of DOC thresholds that determine this coupling. The recent increases in pCO2, linked to shifts in the C balance of lakes, may be contributing to the observed declines in lake pH, leading to a re-acidification of lakes.